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survival_guide [2015/10/07 10:08]
ccrosby created
survival_guide [2015/10/07 15:52] (current)
ccrosby
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 The purpose of this page is to provide the new user with the bare minimum of information required to start using CHPC's facilities. ​ Please explore the rest of the Wiki for more advanced information,​ as well as application-specification instructions and examples. The purpose of this page is to provide the new user with the bare minimum of information required to start using CHPC's facilities. ​ Please explore the rest of the Wiki for more advanced information,​ as well as application-specification instructions and examples.
  
 +===== What you need to know =====
 +  - Most high performance computing (HPC) systems like CHPC's cluster use the Gnu/Linux operating system. ​ Windows applications will not run on the system.
 +  - The computers that make up the HPC cluster do not run faster than a good desktop computer, nor do they usually have particularly impressive amounts of memory. ​ The performance comes from running many compute nodes in parallel. ​ If your application is not parallelised,​ it will not run faster at CHPC than on a good desktop machine.
 +  - The system is designed to be used in batch mode.  The user prepares a job, submits it to the queue, and the system executes it when the requested amount of resources become available.
 +  - You can request an interactive session, which will give you access to a compute node in the cluster. ​ Here you can compile programs, do pre- or post-processing,​ and check your job setup.
 +  - Access to the system is by means of secure-shell (ssh).
 +  - Data can be copied to or from the system by means of secure copy (scp) or rsync.
 +  - Tasks are managed with [[http://​www.pbsworks.com/​|PBS]]
 +  - Although tasks are run in batch mode, the [[howto:​remote_viz|visualisation]] server makes provision for graphical pre- and post-processing.
 +  - Software licensing issues still need to be taken care of appropriately. ​ CHPC hosts academic licenses for some software suites, but for others you will need to make the necessary arrangements with the software vendors.
 +
 +===== Logging in to CHPC =====
 +Once you have a user-id and password, you can log in to the system using ssh.  If you are logging in from a system running a UNIX-like operating system, you can simply use ssh from the command line: ''​ssh myusername@sun.chpc.ac.za''​. ​ From Windows, you can log in using [[https://​cygwin.com/​|Cygwin]] or [[http://​www.putty.org/​|PuTTY]]. Once logged in you can (and should) change your password with the ''​passwd''​ command. ​ Options for logging in are explained in the following [[guide:​connect|guide]].
 +
 +===== The user interface (not) =====
 +Although personal computers running Linux have user interfaces that are very similar to Windows or Mac, the ssh-login to the HPC cluster runs in command line text mode only, by default using the Bash shell. ​ It is therefore essential to master a very small subset of Linux commands. ​ The internet has many excellent resources explaining how to perform tasks in Linux and Bash.  Nevertheless,​ here is a very short summary of the most useful instructions:​
 +  * ls - provide a list of the files in the current directory
 +  * ls -l - provide a more detailed listing of the files in the current directory
 +  * mkdir - create a new directory
 +  * cd - change to a new directory
 +  * rmdir - remove a directory
 +  * rm - remove a file
 +  * vi - start the vi text editor, please refer to  ​
/var/www/wiki/data/attic/survival_guide.1444205318.txt.gz · Last modified: 2015/10/07 10:08 by ccrosby